pdbread

Syntax

Input Arguments

File

Either of the following:

Character vector specifying a file name, a path and
file name, or a URL pointing to a file. The referenced file is a Protein
Data Bank (PDB)-formatted file (ASCII text file). If you specify only
a file name, that file must be on the MATLAB® search path or in
the MATLAB Current Folder.

MATLAB character array that contains the text
of a PDB-formatted file.

Tip

You can use the getpdb function
with the 'ToFile' property to retrieve protein
structure data from the PDB database and create a PDB-formatted file.

ModelNumValue

Positive integer specifying a model in a PDB-formatted
file.

Output Arguments

PDBStruct

MATLAB structure containing a field for each PDB record.

Description

The Protein Data Bank (PDB) database is an archive of experimentally
determined 3-D biological macromolecular structure data. For more
information about the PDB format, see:

PDBStruct = pdbread(File) reads
the data from PDB-formatted text file File and
stores the data in the MATLAB structure, PDBStruct,
which contains a field for each PDB record. The following table summarizes
the possible PDB records and the corresponding fields in the MATLAB structure PDBStruct:

PDB Database Record

Field in the MATLAB Structure

HEADER

Header

OBSLTE

Obsolete

TITLE

Title

CAVEAT

Caveat

COMPND

Compound

SOURCE

Source

KEYWDS

Keywords

EXPDTA

ExperimentData

AUTHOR

Authors

REVDAT

RevisionDate

SPRSDE

Superseded

JRNL

Journal

REMARK 1

Remark1

REMARK N

Note

N equals 2 through 999.

Remarkn

Note

n equals 2 through 999.

DBREF

DBReferences

SEQADV

SequenceConflicts

SEQRES

Sequence

FTNOTE

Footnote

MODRES

ModifiedResidues

HET

Heterogen

HETNAM

HeterogenName

HETSYN

HeterogenSynonym

FORMUL

Formula

HELIX

Helix

SHEET

Sheet

TURN

Turn

SSBOND

SSBond

LINK

Link

HYDBND

HydrogenBond

SLTBRG

SaltBridge

CISPEP

CISPeptides

SITE

Site

CRYST1

Cryst1

ORIGXn

OriginX

SCALEn

Scale

MTRIXn

Matrix

TVECT

TranslationVector

MODEL

Model

ATOM

Atom

SIGATM

AtomSD

ANISOU

AnisotropicTemp

SIGUIJ

AnisotropicTempSD

TER

Terminal

HETATM

HeterogenAtom

CONECT

Connectivity

PDBStruct =
pdbread(File, 'ModelNum', ModelNumValue) reads
only the model specified by ModelNumValue from
the PDB-formatted text file File and
stores the data in the MATLAB structure PDBStruct.
If ModelNumValue does not correspond to
an existing mode number in File, then pdbread reads
the coordinate information of all the models.

The Sequence Field

The Sequence field is also a structure containing
sequence information in the following subfields:

NumOfResidues

ChainID

ResidueNames — Contains
the three-letter codes for the sequence residues.

Sequence — Contains the
single-letter codes for the sequence residues.

Note

If the sequence has modified residues, then the ResidueNames subfield
might not correspond to the standard three-letter amino acid codes.
In this case, the Sequence subfield will contain
the modified residue code in the position corresponding to the modified
residue. The modified residue code is provided in the ModifiedResidues field.

The Model Field

The Model field is also a structure or an
array of structures containing coordinate information. If the MATLAB structure
contains one model, the Model field is a structure
containing coordinate information for that model. If the MATLAB structure
contains multiple models, the Model field is an
array of structures containing coordinate information for each model.
The Model field contains the following subfields:

Atom

AtomSD

AnisotropicTemp

AnisotropicTempSD

Terminal

HeterogenAtom

The Atom Field

The Atom field is also an array of structures
containing the following subfields:

Examples

Use the getpdb function to retrieve
structure information from the Protein Data Bank (PDB) for the nicotinic
receptor protein with identifier 1abt, and then
save the data to the PDB-formatted file nicotinic_receptor.pdb in
the MATLAB Current Folder.

getpdb('1abt', 'ToFile', 'nicotinic_receptor.pdb');

Read the data from the nicotinic_receptor.pdb file
into a MATLAB structure pdbstruct.

pdbstruct = pdbread('nicotinic_receptor.pdb');

Read only the second model from the nicotinic_receptor.pdb file
into a MATLAB structure pdbstruct_Model2.

pdbstruct_Model2 = pdbread('nicotinic_receptor.pdb', 'ModelNum', 2);

View the atomic coordinate information in the model
fields of both MATLAB structures pdbstruct and pdbstruct_Model2.